Here's a place where I can post my thoughts on new papers, provide updates on my projects, and post info that will eventually be on my website The Theropod Database - http://theropoddatabase.com/ . It will center on theropods, but may delve into other topics as well such as phylogenetics.

Tuesday, April 26, 2011

First publication submitted, second in progress

And it's been a while again. Why, you ask? One reason is two weeks ago, I finally got my first paper submitted with David Marjanovic as coauthor. Unlike blog posts, manuscripts require a ton of double-checking and tweaking, so that took quite a while. Now for the peer review process...

And now that my first paper is in the system, I've been working on my second. This one is a detailed reanalysis of the Theropod Working Group matrix. Back on the DML I once praised invertebrate zoologist Ronald Jenner for his paper on how flawed current cladistic practices are. Unfortunately, as you would have gathered from my posts, things have only gotten worse since then. Jenner notes "Rather than representing occasional lapses of judgement, most of the identified errors are symptomatic of a generally cavalier attitude towards character study. A major aim of future cladistic analyses of the Metazoa must therefore be the correction of the many errors through a more detailed and explicit approach to character study." And "It is a striking observation that none of the recent cladistic studies of the Metazoa comprehensively support all data matrix entries with source citations." These are both just as true for theropod analyses.

I figure what better place to start than the TWG matrix? It's accurate in general, uses species-level OTUs, covers a wide and controversial swath of taxa, and most importantly is used by the majority of coelurosaur workers when they describe a new taxon. Over thirty papers have used variants, including over 120 taxa. The goal is not to make a new analysis, since that's a huge long-term project. Instead, the TWG characters (including those from all derivative analyses) will be discussed and refined, but kept as close to their original intent as possible. States will be explicitly and quantitatively defined, and codings will be defended with references to exact specimens or literature. The resulting trees will then be discussed with an emphasis on how parsimonious various alternative topologies are, and how much of the proposed evidence has been incorporated into the dataset.

This way future workers will have a better dataset to plug their taxa into, and any coding disagreements can be more easily resolved. It will also give us a better idea of the current state of coelurosaur phylogenetics and provide suggestions for which characters should be added in future modifications to further our understanding.

Well, this is EXCELLENT news. It surely has been a very long time coming, but I wish you the very best of luck with the review process (and, yes, luck plays a big part). Congratulations on getting it submitted.